Sequence
atgc intronic sequence ATGC exonic sequencegtatgactggaaaagatcattacaaaggaatctttttgcatatgatttacccacggtgtgacaatttgtatgcagGCTTATCTATTCAATGATTACTGGGAAGACATAGGTACTATCAGATCATTCTTTGAGGCAAATCTTGCCCTCACTGAGCAT
Basic information
species | Glycine max |
transcript | GLYMA07G38820.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 3'ss of exon 9
--------------------------------------------------------------------------------------------------------------------gtatgactggaa--aagatcattacaaag---gaatctttttgcatatgatttacccacggt-gtgac----aatttgtatgcagGCTTATCTATTCAATGATTACTGGGAAGACATAGGTACTATCAGATCATTCTTTGAGGCAAATCTTGCCCTCACTGAGCAT
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gtaaggatttaacataataagttccatttggtagtgttctctaatattgcactattggcatcagatttacacaaatttattcaataataatactgcatatgtatgatgtattatttattttcttacaatcaacttcagtatcatgtcagaaactagccttgaacatctcaggcacagttgtaacctagaactcat-tgcagGCATATCTTTTCAATGATTACTGGGAAGACATAGGAACTATAAAATCATTCTTTGAAGCCAATCTTTCTCTTGCTGAACAG
upper sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 5
--------------------------gtatgactggaaaagatcattacaaaggaatctttttgcatatgatttacccacggtgtgacaatttgtatg-cagGCTTATCTATTCAATGATTACTGGGAAGACATAGGTACTATCAGATCATTCTTTGAGGCAAATCTTGCCCTCACTGAGCAT
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actatttgaagacaggcatatcaccatcttagttatgtattcatcctgcctcataatcttgtcccaaaatcttgactt--gatattatgatggacatttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG
upper sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 9
lower sequence: AT5G19220.1 (Arabidopsis thaliana), 3'ss of exon 9
----gtatgactggaaaagatcattacaaaggaatctttttgcatatgatttacccacggtgtgacaa---tttgtatgcagGCTTATCTATTCAATGATTACTGGGAAGACATAGGTACTATCAGATCATTCTTTGAGGCAAATCTTGCCCTCACTGAGCAT
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gtcagtaacattcatattaagcac-acatttaagtccaatgactaacgttatatcaa-gggataacaagattttttgagcagGCTTATCTCTTTAATGACTACTGGGAAGATATAGGAACAATAAGATCTTTCTTCGAGGCGAATCTTGCACTCACTGAGCAT
upper sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 9
-----------------------------------gtatgactggaaaagatcatt-acaaaggaatctttttgcatatg-atttacccacggtgtgacaatttgtatgcagGCTTATCTATTCAATGATTACTGGGAAGACATAGGTACTATCAGATCATTCTTTGAGGCAAATCTTGCCCTCACTGAGCAT
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gtctggatcaactatctaaaatattttattcaaacccatgaacattataaacaaatgatgatgggtacattcgacacttctgttcatctaacaacacacgacacttttgcagGCTTATCTGTTTAATGATTATTGGGAAGACATTGGTACAATCAGATCATTCTTTGAAGCAAACCTTGCCCTTACTGCACAT
upper sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 9
lower sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 10
gtatgactggaaaagatcattacaaaggaatctttttgcat-atgatttacccacggtgtgacaatttgtat-gcagGCTTATCTATTCAATGATTACTGGGAAGACATAGGTACTATCAGATCATTCTTTGAGGCAAATCTTGCCCTCACTGAGCAT
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----------------------gtgggaagtttgtgtgctttgtcttgcattctacgcctaaaacttgatattgcagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTTTTTGACGCTAATCTCGCTCTCACTGCTCAG
upper sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 9
lower sequence: EFJ25399 (Selaginella moellendorffii), 3'ss of exon 9
gtatgactggaaaagatcattacaaaggaatctttttgcatatgatttacccacggtgtgacaatttgtat-gcagGCTTATCTATTCAATGATTACTGGGAAGACATAGGTACTATCAGATCATTCTTTGAGGCAAATCTTGCCCTCACTGAGCAT
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------------gtgggaagttcgtgtgctttgtcttgcat----tctacccc-----taaaacttgatattgcagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTTTTTGACGCTAATCTCGCTCTCACCGCTCAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|11413026|gb|BF425046.1|BF425046EST: ACTTTGGATCAGAGGTTATTCCTGCCTCAGCCAGAGAATTTTACATGAAG GCTTATCTATTCAATGATTACTGGGAAGACATAGGTACTATCAGATCATTC
genomic: ACTTTGGATCAGAGGTTATTCCTGCCTCAGCCAGAGAATTTTACATGAAGgtatgactgg ... ttgtatgcagGCTTATCTATTCAATGATTACTGGGAAGACATAGGTACTATCAGATCATTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacaaaggaatctttttgcatatgatttacccacggtgtgacaatttgtatgcagGCTTATCTATTCAATGATTACTGGGAAGACATAGGTACTATCAGATCATTCTTTGAGGCAAATCTTGCCCTCACTGAGCAT
atatgattta TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgactggaaaagatcattacaaaggaatctttttgcatatgatttacccacggtgtgacaatttgtatgcagGCTTATCTATTCAATGATTACTGGGAAGACATAGGTACTATCAGATCATTCTTTGAGGCAAATCTTGCCCTCACTGAGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA